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Workflow Tour

Guide Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  guide["Capstone docs"]
  section["TOUR"]
  page["Workflow Tour"]
  proof["Proof route"]

  family --> program --> guide --> section --> page
  page -.checks against.-> proof
flowchart LR
  orient["Read the guide boundary"] --> inspect["Inspect the named files, targets, or artifacts"]
  inspect --> run["Run the confirm, demo, selftest, or proof command"]
  run --> compare["Compare output with the stated contract"]
  compare --> review["Return to the course claim with evidence"]

This tour is the executed proof route for the Snakemake capstone. It creates a bundle under artifacts/workflow-tour/ so you can inspect the workflow the same way the course asks you to reason about it: through declared rules, planned jobs, real execution, published outputs, summary evidence, and the core interpretation guides that tell you what each surface is supposed to settle.

If you want a lighter first step, run make walkthrough first. That bundle focuses on the repository guide, rule list, dry-run plan, and public file contract without executing the workflow.

What the tour produces

  • list-rules.txt: the public rule surface exposed by the workflow
  • dryrun.txt: the planned jobs and commands without executing them
  • run.txt: the execution log from the real workflow run
  • summary.txt: Snakemake’s summary view after the run
  • discovered_samples.json: the durable checkpoint artifact that fixed the dynamic sample set
  • publish-manifest.json: the stable publish boundary inventory
  • provenance.json: the reproducibility record for the run
  • summary.tsv and report/index.html: the compact public review surfaces
  • FILE_API.md: the documented publish contract copied into the bundle
  • the core guides: domain, stage, checkpoint, publish review, incident review, profile audit, and exact source routing
  • bundle-manifest.json: the inventory of files packaged into the review bundle itself

How to use it

From the capstone directory:

make walkthrough
make tour

From the repository root:

make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour

What to inspect first

  1. README.md
  2. DOMAIN_GUIDE.md and WORKFLOW_STAGE_GUIDE.md
  3. list-rules.txt and dryrun.txt
  4. CHECKPOINT_GUIDE.md and discovered_samples.json
  5. summary.txt and run.txt
  6. publish-manifest.json, summary.json, summary.tsv, and provenance.json

That order mirrors the course: repository contract, rule surface, planned DAG, resulting evidence, published interface, and reproducibility metadata.

If that route feels too broad, step back to WALKTHROUGH_GUIDE.md. If it feels too narrow, continue into PUBLISH_REVIEW_GUIDE.md or INCIDENT_REVIEW_GUIDE.md depending on the question you are reviewing.

Use EXECUTION_EVIDENCE_GUIDE.md when the blocker is not where the files are, but what each executed evidence surface is actually supposed to prove.